Cells organize and regulate their growth, metabolism, differentiation and survival based, in large part, on external cues or signals such as hormones, growth factors, or molecules presented by neighbouring cells or the external environment. Interactions of proteins with ligands such as other proteins, phospholipids and nucleic acids mediate the internal responses to these external signals. Proteins that regulate intracellular function are generally, but not always, composed of modular domains that regulate protein—protein, protein-phospholipid, and protein-nucleic acid interactions.
A protein modular domain is a sequence of about 50 to 100 amino acids characterized by an ability to fold into the appropriate three-dimensional structure, and to retain its intermolecular binding properties, even in the absence of additional linked polypeptide sequences. A large number of protein modules have been identified. For example, protein modules have been identified that are involved with (i) cellular functions that control cell growth, or induce cell death or inflammation; (ii) the development of the cytoskeleton; (iii) the intracellular anti-microbial machinery of the cell; and (iv) transcriptional assembly.
With the increasing discovery of new protein—protein interactions there is a need for assays to analyze the interactions and identify modulators of the interactions. However, interacting protein domains are inherently difficult to assay. For example, the identification of inhibitors of an interaction may require a thermodynamically unfavorable situation wherein a weakly binding compound must disrupt and then binds to the interface between two tightly bound protein monomers. Therefore, there is a need for effective methods for assaying biomolecular interactions and for identifying substances that modulate the interactions.